MS-SIG 2013 - Galaxy-P and CloudBioLinux

Paradigm Shift?

What is Galaxy?

New Paradigm

What is Galaxy-P?

Why Galaxy for Mass Spec Informatics?

Galaxy-P on the Tool Shed

Galaxy-P Workflows

A web-based bioinformatics data analysis platform

no need to reinvent the wheel

Old Paradigm

"Dual-label workflow"

Tool shed is the "app store" for Galaxy tools, datatypes, & workflows.

nearing end of year 1

Emanating from a larger community, Galaxy is more mature and developing faster than any comparable open source proteomics platform.

Originally designed to address issues in genomic informatics including:

We have assembled these pieces into useful workflows for identification, quantification, proteogenomics, and metaproteomics.

We have contributed many tools and datatypes to the Galaxy tool shed including...

Three year US NSF funded grant to build mass spec & proteomics data analysis platform on top of Galaxy.

ideally suited for systems biology

mzQuantML datatype

• Software accessibility and usability

• Analytical transparency

• Reproducibility

• Scalability

• Share-ability

"Minnesota Two Step"

Various OpenMS

tools and datatypes

New paradigm: “…allows transparent sharing of not only the precise computational details underlying an analysis, but also intent, context, and narrative.” (Goecks et al Genome Biol. 2010, 11: R86.)

4 of 6 talks at the protein identification oral session of ASMS incorporated sequencing data, multi-omic biology can benefit immensely from a multi-omics data analysis platform.

All these tools available.

An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics

(J. Proteome Res., 2013, PMID: 23391308).

Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11: R86.z

with Galaxy...

ConsensusID

Workflows, histories, and pages can be

shared with others or the world.

Scaffold tools and datatypes

MaxQuant tool

More than Galaxy-P

Galaxy-P for Proteogenomics

Three Ways to Galaxy-P

Galaxy-P in the Cloud

Built on CloudBioLinux

Thanks...

For those with more technical savy, our cloud clusters come preloaded with more than just Galaxy-P

Galaxy-P provides an integrated platform for every step

of proteogenomic analysis.

Our public and internal Galaxy-P servers as well as the

cloud images are built with CloudBioLinux.

Large Proteomic Suites

The whole Galaxy and Galaxy-P team at the Minnesota Supercomputing Institute, with special thanks to Anne-Francoise Lamblin.

Trans-proteomic pipeline, OpenMS, crux

Public

Visit bit.ly/galaxyp-cloud to spin up your own Galaxy-P cluster on Amazon's infrastructure today!

usegalaxyp.org

Identification Tools (Standard and Specialized)

• Build target database - download and translate EST databases or perform gene prediction with Augustus.
• Numerous tools for identification and text manipulation.
• Workflow utilizing BLAST to identify novel peptides.
• Tool to assess peptide-spectrum matches and visualize spectra.
• Visualize identified peptides on the genome.

Myrimatch, X! Tandem, OMSSA, TagRecon, Pepitome, PepNovo

Local

getgalaxyp.org

We have contributed numerous enhancements to make this an excellent framework for proteomic and

mass spec data analysis platform.

Validation Tools

Brad Chapman, Dave Clements, Enis Afgan, Jorrit Boekel, Dannon Baker, Nate Coraor, Jeremy Goecks, Ira Cooke, and the rest of the Galaxy and CloudBioLinux communities.

Percolator, Fido, Mayu, psm-eval

Cloud

GUI Applications

bit.ly/galaxyp-cloud

MZmine, PeptideShaker/SearchGUI, TOPPAS, PRIDE Converter, PRIDEInspector

See our ASMS poster on building proteomic

platforms with CloudBioLinux

BioCloudCentral and CloudMan are easy to use web interfaces for launching and managing Galaxy clusters without requiring knowledge of AMIs, ssh keys, or the Unix terminal.

Programming Environments

bit.ly/cloudbiolinux-asms2013

150 step seamless, integrated proteogenomic workflow

This work is funded by the National Science Foundation.

• pyteomics (Python)
• mspire (Ruby)
• R (w/xcms, mzR, FactoMineR, caret, ggplot2, VennDiagram)

@usegalaxyp

Visit ISMB Poster O097 for more information

Bioinformatics

NCBI Blast+, EMBOSS, Augustus, peptide-to-gff

"Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy. Afgan, Chapman, et. al. Current Protocols in Bioinformatics. June, 2012. "

this presentation

bit.ly/galaxyp-mssig2013

Innovative, Reproducible MS-Based Proteomic Informatics in the Cloud for Emerging Applications with Galaxy-P and CloudBioLinux

1

2

1

John M. Chilton*, James E. Johnson, Ebbing P. de Jong, Getiria Onsongo, Benjamin J. Lynch, Pratik D. Jagtap, Timothy J Griffin

1 University of Minnesota Supercomputing Institute, 2 University of Minnesota

* chilton@msi.umn.edu